Beretta 92FS

In "The Cost of Living" (S05E05), Diakos (Adoni Maropis) uses what appears to be a Beretta 92FS when he assaults Stella. The gun is refered to as a "high caliber automatic pistol".
In "No Good Deed" (S05E16), a suspect drops a Beretta 92FS when being detained by Mac.

Desert Eagle Mark XIX

In "Turbulence" (S5E03), Flack finds a Desert Eagle Mark XIX with pearl grips in a hotel room where an Air Marshal was murdered, the suspect apparently used a stuffed animal to suppress the sound of the gunshot.
In "Pay Up" (S5E25), a Desert Eagle Mark XIX is used by a kidnapper to kill Det. Jessica Angell. The kidnapper is seen using it in the climax of the episode, dropping it after being wounded by Flack. Hawkes is also seen holding one while he and Det. Monroe examine the .50AE round discovered at the crime scene.

Desert Eagle Mark XIX - .50 AE Chrome Silver

Det. Flack finds the Desert Eagle. (S05E03)

Flack lays the Desert Eagle on the bed prior to placing in an evidence box. (S05E03)

Kahr K9

In "My Name Is Mac Taylor" (S05E08), David Oka (Kelvin Yu) is seen with what appears to be a Kahr K9.

Kahr K9 standard model with fixed sights - 9x19mm

David holds the gun at. (S05E08)

David holds the gun at. (S05E08)

David holds the gun at. (S05E08)

Luger P08

In "Yahrezit" (S05E22), a Neo-Nazi has several Luger P08 pistols. Another Luger fitted with a bayonet on the barrel is used by an ex-Nazi named Klaus Braun (Ed Asner) to commit a murder. The round doesn't penetrate deeply due to the gunpowder having degraded over the years.

Luger P08 - 9x19mm

Adam and Mac prepare to test the Luger. (S05E22)

Mac stabs a pig with the bayonet fitted on the Luger. (S05E22)

Mac shoot the pig as Adam looks on. (S05E22)

The Neo-Nazi's collection of Lugers and Walthers. (S05E22)

Mauser C96

In "Yahrezit" (S05E22), a German SS officer is seen using a Mauser C96 to execute Jewish prisoners during a flashback.

Mauser C96 - 7.63x25mm Mauser

A German SS officer executes a prisoner with the Mauser. (S05E22)

Mauser 1910 Pocket Pistol

In "Communication Breakdown" (S05E19), what appears to be a Mauser 1910 Pocket Pistol is used by a father to ward off the man sleeping with his daughter. When the gun accidentally discharges it strikes a man on a passing train. The gun is misidentified as a .25 caliber.

1910 Mauser Pocket Pistol - .25 ACP

The daughter hands the gun to Mac. (S05E19)

SIG-Sauer P229

In "Turbulence" (S05E03), an air marshal's SIG-Sauer P229 is found by Adam, identified as a "Sig". The SIG is later seen in a flashback when James Turner (Scott Connors) holds the gun on a flight attendant.

SIG-Sauer P229 - 9x19mm

Adam holds the SIG after finding it in an airplane trashcan. (S05E03)

James holds the gun on a flight attendant during a flashback. (S05E03)

SIG-Sauer P226

In "She's Not There" (S05E14), an ESU officer is seen with a SIG-Sauer P226 in preparation for a raid on a warehouse.

Smith & Wesson Model 65

In "The Past, Present and Murder" (S05E21), a Smith & Wesson Model 65 is found in Dunbrook's (Craig T. Nelson) office. It is identified as a "Smith & Wesson .38 Special" and is seen being test fired by Stella in the lab.

Submachine Gun

Heckler & Koch MP5A2

In "Veritas" (S05E01), plain clothed NYPD officers are seen with Heckler & Koch MP5A2s.
In "Turbulence" (S05E03), ESU officers are seen with Heckler & Koch MP5A2s while the CSIs investigate the murder aboard an airplane.
In "Pay Up" (S05E25), ESU officers are again seen with Heckler & Koch MP5A2s in preparation for the final attack on the kidnappers hideout.

Heckler & Koch MP5A2 with Surefire 628 weaponlight - 9x19mm

An officer aims the MP5A2 at Joe as he is arrested. (S05E01)

An officer holds his MP5A2. (S05E03)

An ESU officer holds his MP5A2 as the prepare to enter the building. (S05E25)

MP40

In "Yahrezit" (S05E22), during a flashback, German SS officers are seen with MP40s.

MP40 - 9x19mm

SS officers prepare to execute Jewish prisoners. (S05E22)

SS officers prepare to execute Jewish prisoners. (S05E22)

Assault Rifles

AKMSU

In "Point of No Return" (S05E18), Little Stevie (Emilio Rivera) fires what appears to be an AKMSU at Danny, Flack and Mac.

Stevie runs down the hallway after firing the AK at Flack and Mac. (S05E18)

AK Rifle

In "Pay Up" (S05E25), a gunman is seen with an AK-style rifle that he used to shoot at Flack, Danny and Mac. The AK is later seen in the ransom video for Dunbrook's son. This rifle has an open front sight like an AKM.

The gunman prepares to take aim with the AK. (S05E25)

The gunman takes cover with the AK. (S05E25)

A kidnapper holds the AK on Dunbrook's son. This rifle has an open front sight like an AKM. (S05E25)

M4A1 Carbine

In "Pay Up" (S05E25), ESU members are seen with M4A1s when storming a garage.

Machine Guns

MG42

The MG42 sits under an Nazi Flag in the hideout of a Neo-Nazi. (S05E22)

Other

DefTech 37mm launcher

In "Page Turner" (S05E02), officers in riot gear fire what are described by Det. Flack as "37mm soft rounds, bean bags" from a DefTech 37mm launcher.

DefTech 37mm launcher

An officer takes aim with the launcher. (S05E02)

An officer takes aim with the launcher. (S05E02)

Another view of the launcher. (S05E02)

Pen Gun

In "The Cost of Living" (S05E05), a custom pen gun which fires a "rimfire .22 caliber" used by the real James Sutton (Chad Faust). It is seen being reconstructed by Sheldon and Mac.

Sheldon shows the "gun" to Mac. (S05E05)

Sheldon fires the "gun". (S05E05)

Remington 870 (Taser)

In "Enough" (S05E06), Det. Stella Bonasera (Melina Kanakaredes) test fires a modified Remington 870 that is supposed to fire taser rounds like the Taser X-12. Stella identifies the rounds as a "wireless charge with 4 barbs that packs a 1500 volt punch for up to 20 seconds." (In reality, this type of modified Remington is used by police departments to fire beanbag rounds.)